Merge branch 'master' of https://git01.codeplex.com/bio

.gitignore

@@ -10,6 +10,4 @@ bio/bin/*
 bio/Tests/Bio.Tests.Web/bin/*
 bio/Tests/Bio.Tests.Web/obj/*
 bio/Tests/Bio.Tests.Pamsam/bin/*
-bio/Tests/Bio.Tests.Padena/bin/*
-
-
+bio/Tests/Bio.Tests.Padena/bin/*

bio/Source/Framework/Bio.Android/Resources/Resource.Designer.cs

@@ -2,7 +2,7 @@
 //------------------------------------------------------------------------------
 // <auto-generated>
 //     This code was generated by a tool.
-//     Runtime Version:4.0.30319.34014
+//     Runtime Version:4.0.30319.0
 //
 //     Changes to this file may cause incorrect behavior and will be lost if
 //     the code is regenerated.

bio/Source/Framework/Bio.Core/IO/BAM/BAMParser.cs

@@ -318,7 +318,7 @@ namespace Bio.IO.BAM
             {
                 var binStart = start >> 14;
                 FileOffset minStart;
-                if (refIndex.Bins.Count <= binStart)
+                if (refIndex.LinearIndex.Count > binStart)
                 {
                     minStart = refIndex.LinearIndex[binStart];
                 }

bio/Source/Framework/Bio.Core/IO/GenBank/GenBankParser.cs

@@ -767,7 +767,7 @@ namespace Bio.IO.GenBank
             }
 
             metadata.Source.Organism.ClassLevels = classLevels;
-            if (classLevels.Trim().Length > 0)
+            if (classLevels.TrimEnd('.').Length > 0)
             {
                 string genus = classLevels.TrimEnd('.').Split(";".ToCharArray(), StringSplitOptions.RemoveEmptyEntries).Last().Trim();
                 if (!genus.Equals(metadata.Source.Organism.Genus.Trim()))

bio/Source/Framework/Bio.Core/Properties/AssemblyInfo.cs

@@ -26,8 +26,8 @@ using System.Runtime.InteropServices;
 // You can specify all the values or you can default the Build and Revision Numbers 
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("2.0.0.0")]
-[assembly: AssemblyFileVersion("2.0.0.0")]
+[assembly: AssemblyVersion("2.0.0.1")]
+[assembly: AssemblyFileVersion("2.0.0.1")]
 
 [assembly:InternalsVisibleTo("Bio.Desktop")]
 [assembly: InternalsVisibleTo("Bio.Android")]

bio/Source/Framework/Shims/Bio.Platform.Helpers.Droid/Resources/Resource.Designer.cs

@@ -2,7 +2,7 @@
 //------------------------------------------------------------------------------
 // <auto-generated>
 //     This code was generated by a tool.
-//     Runtime Version:4.0.30319.34014
+//     Runtime Version:4.0.30319.0
 //
 //     Changes to this file may cause incorrect behavior and will be lost if
 //     the code is regenerated.

bio/Source/Tests/Bio.Tests/Algorithms/Alignment/NUCmer/NUCmerBvtTestCases.cs

@@ -254,6 +254,8 @@ namespace Bio.Tests.Algorithms.Alignment.NUCmer
         [TestCategory("Priority0")]
         public void ValidateNUCmerGetClusters()
         {
+            // NOTE: Nigel ran this test with the same data through mmummer and mgaps and got the same result.
+
             // Gets the reference sequence from the FastA file
             string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
                 Constants.FilePathNode);
@@ -268,7 +270,6 @@ namespace Bio.Tests.Algorithms.Alignment.NUCmer
             var nuc = new Bio.Algorithms.Alignment.NUCmer(seqs1.First()) {
                 LengthOfMUM = 5,
                 MinimumScore = 0,
-                BreakLength = 0
             };
             var clusts = nuc.GetClusters(seqs2.First());
             string clustCount1 = this.utilityObj.xmlUtil.GetTextValue(

bio/Source/Tests/Bio.Tests/IO/GenBank/GenBankTests.cs

@@ -31,6 +31,7 @@ namespace Bio.Tests.IO.GenBank
 
         #region Fields
         private const string _genBankFile_LocusTokenParserTest = @"TestUtils\GenBank\LocusTokenParserTest.gb";
+        private const string _genBankFile_EmptyOrganismClassificationTest = @"TestUtils\GenBank\EmptyOrganismClassificationTest.gb";
         private const string _genBankFile_WithTPAPrimaryData = @"TestUtils\GenBank\BK000016-tpa.gbk";
         private const string    _genBankFile_WithMultipleDBLines = @"TestUtils\GenBank\seq1.gbk";
         private const string _genBankFile_WithREFSEQPrimaryData = @"TestUtils\GenBank\NM_001747.gb";
@@ -267,6 +268,21 @@ ORIGIN
             Assert.IsNotNull(seq);
         }
 
+        /// <summary>
+        /// This test used to fail.  The sequence is in a GenBank format and would fail if the classification of the 
+        /// ORGANISM was empty (a line with a single dot).
+        /// </summary>
+        [TestMethod]
+        [Priority(0)]
+        [TestCategory("Priority0")]
+        public void TestGenBankEmptyOrganismClassification()
+        {
+            // parse
+            GenBankParser parser = new GenBankParser();
+            ISequence seq = parser.Parse(_genBankFile_EmptyOrganismClassificationTest).FirstOrDefault();
+            Assert.IsNotNull(seq);
+        }
+
         /// <summary>
         /// Verifies that the parser throws an exception when calling ParseOne on a file containing
         /// more than one sequence.

bio/Source/Tests/TestData/TestData.projitems

@@ -366,6 +366,7 @@
     <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBankRepeatRegion.gbk" />
     <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBank\BK000016-tpa.gbk" />
     <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBank\D12555.gbk" />
+    <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBank\EmptyOrganismClassificationTest.gb" />
     <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBank\LocusTokenParserTest.gb" />
     <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBank\NC_001284.gbk" />
     <None Include="$(MSBuildThisFileDirectory)TestUtils\GenBank\NC_003070.gbk" />

bio/Source/Tests/TestData/TestUtils/GenBank/EmptyOrganismClassificationTest.gb

@@ -0,0 +1,30 @@
+LOCUS       AAB24880     74 aa            linear   PRI 08-MAY-1993
+DEFINITION  zinc finger [Homo sapiens].
+ACCESSION   AAB24880
+VERSION     AAB24880.1  GI:263346
+DBSOURCE    accession S52506.1
+KEYWORDS    .
+SOURCE      Homo sapiens (human)
+  ORGANISM  Homo sapiens
+            .
+REFERENCE   1  (residues 1 to 74)
+  AUTHORS   Saleh,M., Selleri,L., Little,P.F. and Evans,G.A.
+  TITLE     Isolation and expression of linked zinc finger gene clusters on
+            human chromosome 11q
+  JOURNAL   Genomics 14 (4), 970-978 (1992)
+   PUBMED   1339395
+  REMARK    GenBank staff at the National Library of Medicine created this
+            entry [NCBI gibbsq 122386] from the original journal article.
+COMMENT     Method: conceptual translation supplied by author.
+FEATURES             Location/Qualifiers
+     source          1..74
+                     /organism="Homo sapiens"
+                     /db_xref="taxon:9606"
+     Protein         1..74
+                     /name="zinc finger"
+     CDS             1..74
+                     /gene="ZNF123"
+                     /coded_by="S52506.1:1..222"
+ORIGIN      
+        1 tgekpfackg ckkafdqkit liqhegvhtg ekpyecrrcg spsagvetsl cirshtlkrh
+       61 pfkhrashyq ahyt

bio/Source/Tests/TestData/TestUtils/NUCmerTestsConfig.xml

@@ -190,7 +190,7 @@
     <MinimumScore>0</MinimumScore>
     <FixedSeparation>0</FixedSeparation>
     <MUMAlignLength>8</MUMAlignLength>
-    <ClustCount1>529</ClustCount1>
+    <ClustCount1>530</ClustCount1>
     <ClustCount2>518</ClustCount2>
     <AlphabetName>Dna</AlphabetName>
     <EdgeStartIndexes>TestUtils\Medium_Size_Start_Index.txt</EdgeStartIndexes>

bio/bioAlgorithms.nuspec

@@ -2,7 +2,7 @@
 <package xmlns="http://schemas.microsoft.com/packaging/2010/07/nuspec.xsd">
   <metadata minClientVersion="2.7.2">
 	<id>NetBioAlgorithms.PCL</id>
-	<version>2.0.140627</version>
+	<version>2.0.141118</version>
 	<authors>Various authors</authors>
 	<owners>The Outercurve Foundation</owners>
 	<licenseUrl>http://bio.codeplex.com/license</licenseUrl>
@@ -18,7 +18,7 @@
 	<tags>bioinformatics biology FASTA FASTQ GenBank nucleotides genomics .NET</tags>
 	<dependencies>
 		<group>
-			<dependency id="NetBioCore.PCL" version="2.0.140627" />
+			<dependency id="NetBioCore.PCL" version="2.0.141118" />
 		</group>
 	  <!--<group targetFramework="...">
 		<dependency id="Microsoft.Bcl.Async" version="1.0.168" />

bio/bioCore.nuspec

@@ -2,7 +2,7 @@
 <package xmlns="http://schemas.microsoft.com/packaging/2010/07/nuspec.xsd">
   <metadata minClientVersion="2.7.2">
     <id>NetBioCore.PCL</id>
-    <version>2.0.140630</version>
+    <version>2.0.141118</version>
     <authors>Various authors</authors>
     <owners>The Outercurve Foundation</owners>
     <licenseUrl>http://bio.codeplex.com/license</licenseUrl>

bio/bioWeb.nuspec

@@ -2,7 +2,7 @@
 <package xmlns="http://schemas.microsoft.com/packaging/2010/07/nuspec.xsd">
   <metadata minClientVersion="2.7.2">
 	<id>NetBioWeb.PCL</id>
-	<version>2.0.140627</version>
+	<version>2.0.141118</version>
 	<authors>Various authors</authors>
 	<owners>The Outercurve Foundation</owners>
 	<licenseUrl>http://bio.codeplex.com/license</licenseUrl>
@@ -18,7 +18,7 @@
 	<tags>bioinformatics biology FASTA FASTQ GenBank nucleotides genomics .NET</tags>
 	<dependencies>
 		<group>
-			<dependency id="NetBioCore.PCL" version="2.0.140627" />
+			<dependency id="NetBioCore.PCL" version="2.0.141118" />
 		</group>
 	  <!--<group targetFramework="...">
 		<dependency id="Microsoft.Bcl.Async" version="1.0.168" />